Be sure to look up the doc on every metadata format to see if it says anything about default encoding. I would think that ogg and flac metadata has a default encoding(utf8 maybe?). For mp3/id3 on the other hand, I don't think the standard specifies anything, but I would recommend you to double-check that.
I've also seen some mp3-tags where there is an encoding string at the beginning. Don't know how common that is, but maybe it's something to examine further?
I would use UTF-8 as much as possible, and convert to (and from) utf8 only at the input (and output). The database should already be utf8, so from what I understand, option 1 seems the best. Maybe even default to latin1 for metadata formats that doesn't have a standard encoding?